Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

Summary
The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix (G) is replaced by an approximation of G−1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G−1 and the approximated G−1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G−1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was re...

Source: Journal of Animal Breeding and Genetics - April 1, 2015 Category: Genetics & Stem Cells Authors: B.O. Fragomeni, D.A.L. Lourenco, S. Tsuruta, Y. Masuda, I. Aguilar, I. Misztal Tags: Original Article Source Type: research